Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 583 to 632 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
583	OPN4	opsin 4 (melanopsin). [source:swissprot;acc:q9uhm6]	237.28	252.492	1.06411	
584	TLX2	t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [source:swissprot;acc:o43763]	237.28	252.492	1.06411	
585	TLX1	t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [source:swissprot;acc:p31314]	237.28	252.492	1.06411	
586	HECTD1	hect domain containing protein 1 (fragment). [source:swissprot;acc:q9ult8]	237.28	252.492	1.06411	
587	BARX2	homeobox protein barh-like 2. [source:swissprot;acc:q9umq3]	237.28	252.492	1.06411	
588	SBDS	shwachman-bodian-diamond syndrome protein (cgi-97). [source:swissprot;acc:q9y3a5]	216.557	230.362	1.06375	
589		u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [source:swissprot;acc:q9y333]	228.215	214.546	1.06371	
590	RRM1	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [source:swissprot;acc:p23921]	217.215	204.279	1.06333	
591	RPP30	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [source:swissprot;acc:p78346]	216.72	230.439	1.0633	
592	PPP1R7	protein phosphatase 1, regulatory subunit 7; sds22. [source:refseq;acc:nm_002712]	91.63	97.4011	1.06298	
593	DR1	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [source:swissprot;acc:q01658]	232.118	218.406	1.06278	
594	CDC40	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [source:swissprot;acc:o60508]	223.282	210.136	1.06256	
595	VAV1	vav proto-oncogene. [source:swissprot;acc:p15498]	212.2	199.849	1.0618	
596	VAV3	vav-3 protein. [source:swissprot;acc:q9ukw4]	212.253	199.908	1.06175	
597	VAV2	vav-2 protein. [source:swissprot;acc:p52735]	212.526	200.212	1.0615	
598	AKT1	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [source:swissprot;acc:p31749]	248.463	234.095	1.06138	
599	AKT3	rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [source:swissprot;acc:q9y243]	248.463	234.095	1.06138	
600	AKT2	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [source:swissprot;acc:p31751]	248.463	234.095	1.06138	
601	VPS39	vam6/vps39-like protein (hvam6p). [source:swissprot;acc:q96jc1]	206.274	218.792	1.06069	
602	MAP4	microtubule-associated protein 4 (map 4). [source:swissprot;acc:p27816]	206.274	218.792	1.06069	
603	LEF1	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [source:swissprot;acc:q9uju2]	225.829	212.945	1.0605	
604	RPL15	60s ribosomal protein l15. [source:swissprot;acc:p39030]	217.862	230.978	1.0602	
605	HIST1H2BL	histone h2b.c (h2b/c). [source:swissprot;acc:q99880]	247.47	233.441	1.0601	
606	HIST2H2BA	histone h2b.q (h2b/q) (h2b-gl105). [source:swissprot;acc:q16778]	247.47	233.441	1.0601	
607		histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [source:swissprot;acc:p16106]	247.47	233.441	1.0601	
608		histone h2b. [source:refseq;acc:nm_175055]	247.47	233.441	1.0601	
609		histone h2b.s (h2b/s). [source:swissprot;acc:p57053]	247.47	233.441	1.0601	
610		histone h2b.d (h2b/d). [source:swissprot;acc:q99877]	247.47	233.441	1.0601	
611	HIST3H3	histone h3.4 (h3t) (h3/t) (h3/g). [source:swissprot;acc:q16695]	247.47	233.441	1.0601	
612	HIST1H2BA	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [source:refseq;acc:nm_170610]	247.47	233.441	1.0601	
613		histone h2b.e (h2b/e). [source:swissprot;acc:q99879]	247.47	233.441	1.0601	
614	HOXA10	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [source:swissprot;acc:p31260]	214.257	202.125	1.06002	
615	HOXB9	homeobox protein hox-b9 (hox-2e) (hox-2.5). [source:swissprot;acc:p17482]	214.257	202.132	1.05999	
616	HOXA9	homeobox protein hox-a9 (hox-1g). [source:swissprot;acc:p31269]	214.257	202.132	1.05999	
617	HOXC9	homeobox protein hox-c9 (hox-3b). [source:swissprot;acc:p31274]	214.257	202.135	1.05997	
618	GABRG3	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q99928]	214.256	202.139	1.05994	
619	FOXG1	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [source:swissprot;acc:q14488]	214.256	202.139	1.05994	
620	GABRG1	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q8n1c3]	214.256	202.14	1.05994	
621	GABRA2	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p47869]	214.256	202.14	1.05994	
622	GABRA6	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q16445]	214.256	202.14	1.05994	
623	GABRG2	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p18507]	214.256	202.14	1.05994	
624		interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [source:refseq;acc:nm_016123]	214.256	202.139	1.05994	
625	GABRA4	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p48169]	214.256	202.14	1.05994	
626	GABRE	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [source:swissprot;acc:p78334]	214.256	202.14	1.05994	
627	JMJD6	phosphatidylserine receptor; phosphatidylserine receptor beta. [source:refseq;acc:nm_015167]	214.256	202.139	1.05994	
628	GABRA1	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p14867]	214.256	202.14	1.05994	
629	GABRA3	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p34903]	214.256	202.14	1.05994	
630	NDUFA6	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [source:swissprot;acc:p56556]	214.256	202.141	1.05993	
631	PDXDC1	similar to expressed sequence aa415817. [source:sptrembl;acc:q8n4q9]	214.256	202.141	1.05993	
632	HOXD9	homeobox protein hox-d9 (hox-4c) (hox-5.2). [source:swissprot;acc:p28356]	214.254	202.166	1.05979	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/